I think I have old Nikon Sales manuals which show the Nikkor-N has slightly different optical dimensions from the K (New Nikkor) and AI versions. But they are very similar.
The Nikkor-N 35/1.4 also had a similar minor change in spacing, curvature and glass material when upgraded to the K version. As you know, the the Nikkor-N 35/1.4 has slightly radioactive glass which turns yellow over time. I haven't head that the Nikkor-N 28/2 has the same problem.
The AI-S 28/2 has a closer focus limit than the AI and other previous versions, so it is possible the optics were revised again although they remain very similar. The drawings I have are not detailed enough to confirm one way or the other. It's also possible Nikon kept the optics the same and simply extended the focus/CRC range a bit further. Some reviewers suggest the AI version may be slightly better, but it's hard to say if it's sample variation or if the optics really did change.